Benjamin Pierce's father died when he was six. He subsequently worked on his uncle's farm until enlisting in Ebenezer Bridge’s Massachusetts regiment on April 26, 1775.

On May 24, 1787, he married Elizabeth Andrews. Their daughter, named Elizabeth Andrews Pierce, was born August 9, 1788, but the elder Elizabeth died of childbirth complications four days later on August 13. Elizabeth Andrews Pierce (1788–1855) was the wife of Army General John McNeil Jr.

He married Anna Kendrick (born October 30, 1769) on February 1, 1790 at Amherst, New Hampshire. Together they had eight children:

John Sullivan Pierce (November 5, 1796 – September 28, 1824), a first lieutenant in the Army who served at Fort Mackinac and other posts in Michigan, and died in Detroit.

Harriet B. Pierce (1800–1837)

Charles Grandison Pierce (1803–1828)

Franklin Pierce (November 23, 1804 – 1869), 14th President of the United States

Charlotte Pierce, d. in infancy.

Henry Dearborn Pierce (September 19, 1812 – 1880)

They remained married until her death on December 7, 1838. He died 4 months later in Hillsborough, and is buried in the town's Pine Hill Cemetery.

Benjamin Pierce was an original member of the Massachusetts Society of the Cincinnati with membership inherited through primogeniture. His eldest son, Benjamin Kendrick Pierce, succeeded him as a member in the society in 1841. He was then succeeded by his younger brother, future president Franklin Pierce in 1852, and was later succeeded by Benjamin's youngest son, Henry Dearborn Pierce in 1873.